rs7111898

Variant names:

• chr11-13187828-T-C
• rs7111898
• ENST00000741297.1:n.95-6317A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000741297.1(ENSG00000296717):​n.95-6317A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.541 in 151,946 control chromosomes in the GnomAD database, including 23,346 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.54 (23346 hom., cov: 32)
• Consequence: ENSG00000296717 ENST00000741297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.147
• Publications: 2 publications found

Genes affected

ENSG00000296717 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296717	ENST00000741297.1	n.95-6317A>G		intron_variant	Intron 1 of 3
ENSG00000296717	ENST00000741299.1	n.80-6317A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.541 AC: 82137 AN: 151830 Hom.: 23351 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.564

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.541 AC: 82154 AN: 151946 Hom.: 23346 Cov.: 32 AF XY: 0.532 AC XY: 39506 AN XY: 74266

African (AFR) AF: 0.385 AC: 15939 AN: 41438

American (AMR) AF: 0.586 AC: 8944 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2252 AN: 3472

East Asian (EAS) AF: 0.351 AC: 1818 AN: 5174

South Asian (SAS) AF: 0.427 AC: 2064 AN: 4832

European-Finnish (FIN) AF: 0.507 AC: 5339 AN: 10534

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.644 AC: 43735 AN: 67924

Other (OTH) AF: 0.560 AC: 1183 AN: 2112

Alfa AF: 0.606 Hom.: 13891

Bravo AF: 0.542

Asia WGS AF: 0.394 AC: 1370 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.1
DANN	Benign	0.92
PhyloP100		0.15

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7111898; hg19: chr11-13209375;